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Seyfert CE, Porten C, Yuan B, Deckarmb S, Panter F, Bader CD, Coetzee J, Deschner F, Tehrani KHME, Higgins PG, Seifert H, Marlovits T, Herrmann J, Müller R. Darobactins Exhibiting Superior Antibiotic Activity by Cryo‐EM Structure Guided Biosynthetic Engineering. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202217800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Carsten E. Seyfert
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Christoph Porten
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Biao Yuan
- University Medical Center Hamburg-Eppendorf (UKE) Institute of Structural and Systems Biology Notkestraße 85, Building 15 22607 Hamburg Germany
- Centre for Structural Systems Biology (CSSB) Hamburg Germany
| | - Selina Deckarmb
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Fabian Panter
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Chantal D. Bader
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Janetta Coetzee
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Felix Deschner
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Kamaleddin H. M. E. Tehrani
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Paul G. Higgins
- Microbiology, Immunology and Hygiene Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne Germany
| | - Harald Seifert
- Microbiology, Immunology and Hygiene Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne Germany
| | - Thomas Marlovits
- University Medical Center Hamburg-Eppendorf (UKE) Institute of Structural and Systems Biology Notkestraße 85, Building 15 22607 Hamburg Germany
- Centre for Structural Systems Biology (CSSB) Hamburg Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY) Hamburg Germany
| | - Jennifer Herrmann
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Rolf Müller
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
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Seyfert CE, Porten C, Yuan B, Deckarmb S, Panter F, Bader CD, Coetzee J, Deschner F, Tehrani KHME, Higgins PG, Seifert H, Marlovits T, Herrmann J, Müller R. Darobactins Exhibiting Superior Antibiotic Activity by Cryo‐EM Structure Guided Biosynthetic Engineering. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202217800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Carsten E. Seyfert
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Christoph Porten
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Biao Yuan
- University Medical Center Hamburg-Eppendorf (UKE) Institute of Structural and Systems Biology Notkestraße 85, Building 15 22607 Hamburg Germany
- Centre for Structural Systems Biology (CSSB) Hamburg Germany
| | - Selina Deckarmb
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Fabian Panter
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Chantal D. Bader
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Janetta Coetzee
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Felix Deschner
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Kamaleddin H. M. E. Tehrani
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Paul G. Higgins
- Microbiology, Immunology and Hygiene Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne Germany
| | - Harald Seifert
- Microbiology, Immunology and Hygiene Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne Germany
| | - Thomas Marlovits
- University Medical Center Hamburg-Eppendorf (UKE) Institute of Structural and Systems Biology Notkestraße 85, Building 15 22607 Hamburg Germany
- Centre for Structural Systems Biology (CSSB) Hamburg Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY) Hamburg Germany
| | - Jennifer Herrmann
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Rolf Müller
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
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Seyfert CE, Porten C, Yuan B, Deckarm S, Panter F, Bader C, Coetzee J, Deschner F, Tehrani K, Higgins PG, Seifert H, Marlovits T, Herrmann J, Müller R. Darobactins Exhibiting Superior Antibiotic Activity by Cryo‐EM Structure Guided Biosynthetic Engineering. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202214094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carsten E Seyfert
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Christoph Porten
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Biao Yuan
- University Medical Center Hamburg-Eppendorf: Universitatsklinikum Hamburg-Eppendorf Institute of Structural and Systems Biology GERMANY
| | - Selina Deckarm
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Fabian Panter
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Chantal Bader
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Janetta Coetzee
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Felix Deschner
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Kamaleddin Tehrani
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Paul G Higgins
- Uniklinik Köln Microbiology, Immunology and Hygiene GERMANY
| | - Harald Seifert
- Uniklinik Köln Microbiology, Immunology and Hygiene GERMANY
| | - Thomas Marlovits
- Universitätsklinikum Hamburg-Eppendorf Institute of Structural and Systems Biology GERMANY
| | - Jennifer Herrmann
- Helmholtz-Institut für Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland Microbial Natural Products Campus Building E8.1 66123 Saarbrücken GERMANY
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Guo EZ, Desrosiers DC, Zalesak J, Tolchard J, Berbon M, Habenstein B, Marlovits T, Loquet A, Galán JE. A polymorphic helix of a Salmonella needle protein relays signals defining distinct steps in type III secretion. PLoS Biol 2019; 17:e3000351. [PMID: 31260457 PMCID: PMC6625726 DOI: 10.1371/journal.pbio.3000351] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/12/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022] Open
Abstract
Type III protein-secretion machines are essential for the interactions of many pathogenic or symbiotic bacterial species with their respective eukaryotic hosts. The core component of these machines is the injectisome, a multiprotein complex that mediates the selection of substrates, their passage through the bacterial envelope, and ultimately their delivery into eukaryotic target cells. The injectisome is composed of a large cytoplasmic complex or sorting platform, a multiring base embedded in the bacterial envelope, and a needle-like filament that protrudes several nanometers from the bacterial surface and is capped at its distal end by the tip complex. A characteristic feature of these machines is that their activity is stimulated by contact with target host cells. The sensing of target cells, thought to be mediated by the distal tip of the needle filament, generates an activating signal that must be transduced to the secretion machine by the needle filament. Here, through a multidisciplinary approach, including solid-state NMR (SSNMR) and cryo electron microscopy (cryo-EM) analyses, we have identified critical residues of the needle filament protein of a Salmonella Typhimurium type III secretion system that are involved in the regulation of the activity of the secretion machine. We found that mutations in the needle filament protein result in various specific phenotypes associated with different steps in the type III secretion process. More specifically, these studies reveal an important role for a polymorphic helix of the needle filament protein and the residues that line the lumen of its central channel in the control of type III secretion.
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Affiliation(s)
- Emily Z. Guo
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Daniel C. Desrosiers
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Jan Zalesak
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - James Tolchard
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN-CNRS Université de Bordeaux, Pessac, France
| | - Mélanie Berbon
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN-CNRS Université de Bordeaux, Pessac, France
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN-CNRS Université de Bordeaux, Pessac, France
| | - Thomas Marlovits
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE) and German Electron Synchrotron Centre (DESY), Hamburg, Germany
| | - Antoine Loquet
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN-CNRS Université de Bordeaux, Pessac, France
| | - Jorge E. Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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Smaldone G, Pirone L, Pedone E, Marlovits T, Vitagliano L, Ciccarelli L. The BTB domains of the potassium channel tetramerization domain proteins prevalently assume pentameric states. FEBS Lett 2016; 590:1663-71. [PMID: 27152988 DOI: 10.1002/1873-3468.12203] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 01/05/2023]
Abstract
Potassium channel tetramerization domain-containing (KCTD) proteins are involved in fundamental physio-pathological processes. Here, we report an analysis of the oligomeric state of the Bric-à-brack, Tram-track, Broad complex (BTB) domains of seven distinct KCTDs belonging to five major clades of the family evolution tree. Despite their functional and sequence variability, present electron microscopy data highlight the occurrence of well-defined pentameric states for all domains. Our data also show that these states coexist with alternative forms which include open pentamers. Thermal denaturation analyses conducted using KCTD1 as a model suggest that, in these proteins, different domains cooperate to their overall stability. Finally, negative-stain electron micrographs of KCTD6(BTB) in complex with Cullin3 show the presence of assemblies with a five-pointed pinwheel shape.
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Affiliation(s)
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy.,Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (C.I.R.C.M.S.B.), Catania, Italy
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
| | - Thomas Marlovits
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
| | - Luciano Ciccarelli
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
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Marlovits T. EM of Pathogen Secretion Systems: Unfolded Protein Transport across Membranes in Action. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.488.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thomas Marlovits
- Institute for Structural and Systems Biology Center for Structural Systems BiologyUniversity Medical Center Hamburg‐Eppendorf and German Electron Synchrotron CenterHamburgGermany
- IMP Research Institute of Molecular PathologyViennaAustria
- Institute of Molecular Biotechnology Austrian Academy of SciencesViennaAustria
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DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V, Egelman E, Marlovits T, Cheng Y, Baker D. Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Nat Methods 2015; 12:361-365. [PMID: 25707030 PMCID: PMC4382417 DOI: 10.1038/nmeth.3286] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 12/11/2014] [Indexed: 12/12/2022]
Abstract
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.
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Affiliation(s)
- Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Yifan Song
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Cyrus Biotechnology, Inc., Seattle, WA, USA
| | - Xueming Li
- Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Matthias J Brunner
- Center for Structural Systems Biology (CSSB) University Medical Center Eppendorf-Hamburg (UKE), Hamburg, Germany.,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Chunfu Xu
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | | | - Edward Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Thomas Marlovits
- Center for Structural Systems Biology (CSSB) University Medical Center Eppendorf-Hamburg (UKE), Hamburg, Germany.,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Yifan Cheng
- Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
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